Opjose,
There could certainly have been code to detect modchips in the beta versions sent by MS. Every time you played a game it may have sent the crc info of your bios or perhaps some other flag to MS which they were ignoring until 2 days ago. There is no need for a software download to enable something which may have been existing already. This seems even more likely given the fact that NFL 2k3 was still working for many people. It was not one of the demos sent out, and was released much much earlier. It probably had no code to check for chips.
It is also pretty hard to dispute the fact that on the same xbox, people can't connect with modchip enabled, but can when they disable it. My friends xbox works the exact same way. We toggled it like 5 times on separate days and every time the chip was enabled, we could not log in to live, but once we disabled it, it worked like a charm. It's hard to believe that it could be caused by server issues so repeatably on different days.
Yes the servers are unstable right now and for the past couple of days. That has definately been confusing the issue, but it does seem likely that they are detecting modchips. It's no big deal. Just need to disable it.
What is most interesting is the fact that some people cannot connect even when they disable it. That is the only real mystery here. Perhaps that is just server issues.